|
| Status |
Public on Nov 14, 2021 |
| Title |
RB8: dKO_E4 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 chimera
population: GP66:I-Ab+ Rosa26YFP+ CD4+ spleen T cells
infection: LCMV Arm d7 pi
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
WT/dKO_E4: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 P3 run and combined with a previous NextSeq 2000 P2 run. The sequencing run was setup as a 2x51 cycles symmetric run. R1: 51bp, Index1: 8bp, Index2: 16bp, R2: 51bp. WT/dKO_E5/E6/E7: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 run. The sequencing run was setup as a 50 cycles + 50 cycles symmetric run. R1: 50bp, Index1: 8bp, Index2: 16bp, R2: 50bp.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Basecalling was done with RTA 3.9.2 for WT/dKO_E4/E5, with RTA 3.7.17 for WT/dKO_E6 and with RTA 2.4.11 for WT/dKO_E7.
Barcode was demultiplexed allowing 1 mismatch with Bcl2fastq 2.20.
Alignment, tagging and accessibility counting were done with Cellranger ATAC 1.2.0.
Genome_build: mm10
|
| |
|
| Submission date |
Sep 27, 2021 |
| Last update date |
Nov 15, 2021 |
| Contact name |
Remy Bosselut |
| E-mail(s) |
[email protected]
|
| Organization name |
National Cancer Institute, National Institute of Health
|
| Department |
Laboratory of Immune Cell Biology
|
| Lab |
Bosselut
|
| Street address |
9000 Rockville Pike, Building 37
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE184846 |
Dependence on Bcl6 and Blimp1 identifies distinct mechanisms driving memory and follicular helper CD4+ T cell differentiation [scATAC-Seq] |
| GSE184848 |
Dependence on Bcl6 and Blimp1 identifies distinct mechanisms driving memory and follicular helper CD4+ T cell differentiation |
|
| Relations |
| SRA |
SRX12375246 |
| BioSample |
SAMN21856569 |
